On usually refers to being in contact with the surface of something, and in usually refers to being surrounded by something and so would be mutually exclusive
When you ride a mass-transit vehicle, you can stand up in it (at least when it's not moving). So on makes sense here. Especially buses - some might have standing room only. You will both be on and in the bus.
The same thing with a chair - a chair with armrests and a high back will surround you on all sides, but you are also atop the seat, so both in and on apply, depending on the type of chair. You wouldn't be in a barstool, but you'd definitely be in a recliner.
Except through repeated usage, is there a way to anticipate what the exceptions might be?
Not really. The "right" preposition with certain verbs and categories of nouns - especially certain nouns that don't refer to physical objects - is effectively arbitrary and needs to just be learned.
Speaking in French is a great example. You can invent situations to help you remember - perhaps a person who isn't familiar with a foreign language feels "surrounded" by the words in some sense.
Some hints and patterns:
An authority figure can put you on various states of freedom/grace - on vacation, on leave, on notice, on punishment, on administrative leave, etc.
Topics of conversation or meaning are something one is on.
Emotional states are something one is in - in love, in sadness, in madness, in good spirits, in ecstasy.